{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:53Z","timestamp":1772138093995,"version":"3.50.1"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2019,3,29]],"date-time":"2019-03-29T00:00:00Z","timestamp":1553817600000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 GM088344"],"award-info":[{"award-number":["R01 GM088344"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DBI-0939454"],"award-info":[{"award-number":["DBI-0939454"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000183","name":"Army Research Office","doi-asserted-by":"publisher","award":["W911NF-12-1-0390"],"award-info":[{"award-number":["W911NF-12-1-0390"]}],"id":[{"id":"10.13039\/100000183","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Texas Advanced Computing Center"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Stochastic gene expression simulations often assume steady-state transcript levels, or they model transcription in more detail than translation. Moreover, they lack accessible programing interfaces, which limit their utility.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We present Pinetree, a step-wise gene expression simulator with codon-specific translation rates. Pinetree models both transcription and translation in a stochastic framework with individual polymerase and ribosome-level detail. Written in C++ with a Python front-end, any user familiar with Python can specify a genome and simulate gene expression. Pinetree was designed to be efficient and scale to simulate large plasmids or viral genomes.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Pinetree is available on GitHub (https:\/\/github.com\/benjaminjack\/pinetree) and the Python Package Index (https:\/\/pypi.org\/project\/pinetree\/).<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz203","type":"journal-article","created":{"date-parts":[[2019,3,27]],"date-time":"2019-03-27T17:26:30Z","timestamp":1553707590000},"page":"4176-4178","source":"Crossref","is-referenced-by-count":13,"title":["Pinetree: a step-wise gene expression simulator with codon-specific translation rates"],"prefix":"10.1093","volume":"35","author":[{"given":"Benjamin R","family":"Jack","sequence":"first","affiliation":[{"name":"Department of Integrative Biology, The University of Texas at Austin , Austin, TX, USA"}]},{"given":"Claus O","family":"Wilke","sequence":"additional","affiliation":[{"name":"Department of Integrative Biology, The University of Texas at Austin , Austin, TX, USA"}]}],"member":"286","published-online":{"date-parts":[[2019,3,28]]},"reference":[{"key":"2023020108351126800_btz203-B1","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1002\/(SICI)1097-0290(19970720)55:2<375::AID-BIT15>3.0.CO;2-G","article-title":"Intracellular kinetics of a growing virus: a genetically structured simulation for bacteriophage T7","volume":"55","author":"Endy","year":"1997","journal-title":"Biotechnol. 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